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Day: 20120810

ScienceDaily (Aug. 9, 2012) — Researchers at the Freie Universität Berlin, Germany and the Center for Genomic Regulation (CRG) in Barcelona, Spain have designed open source software that allows tracking the position of Drosophila fruit flies as well as their larvae during behavioral experiments.

The research appeared in two joint publications in the open access journal PLoS ONE.

Dr. Matthieu Louis, the head of the Spanish team explains: “Until we developed these tools, many researchers relied on expensive commercial hardware and software to study the behavior of larvae and adult flies. Now, virtually anybody can do this kind of research. The value of the software we are proposing is that they are written in a simple programming language, which facilitates their adaptation to new experimental paradigms” Inexpensive, ubiquitous digital cameras, such as webcams are sufficient to capture the movements of the animals and the open source software packages both for the evaluation the video feeds for tracking as well as for later data analysis are available for free (http://buridan.sourceforge.net).

“Apart from ruining your glass of expensive red wine, Drosophila is a central model organism to study, amongst other problems, how brains work. By carefully watching whether flies turn left or right, we aim at understanding how humans make decisions” explained Dr. Alejandro Gomez-Marin, first author in the Spanish team.

The data and tools provided with their publications will allow researchers to not only improve the accuracy of the research results, but also to develop new analysis methods, “maybe someone will come up with an analysis we would have never thought about” hopes Dr. Gomez-Marin. “We have already received several emails from people who are already using our software packages, even before they were officially published” says Dr. Julien Colomb, first author in the German team “it’s exciting to see other colleagues adopting the tools we developed, because they’re easy to access and free.”

The work presented in the two publications is part of a growing movement pushing for Open Science where publicly funded research data become freely accessible. “Opening up some of the research tools is only a first step,” says Dr. Colomb, “The next step in our efforts to promote open science is to make the data available online, not only before being published, but automatically while analyzed. And we are working on it.” Ultimately, the blueprints for the various experimental containers in which these experiments take place will be translated into a computer-readable format such that 3D printers can re-create the exact experimental conditions anywhere in the world.

“Eventually, I’d like to get everything to be so simple and cheap that anybody would have the chance to do these experiments, even the high school student with fruit flies in the kitchen.” said Dr. Björn Brembs, head of the German team.

ScienceDaily (Aug. 9, 2012) — The sought-after equanimity of “living in the moment” may be impossible, according to neuroscientists who’ve pinpointed a brain area responsible for using past decisions and outcomes to guide future behavior. The study, based on research conducted at the University of Pittsburgh and published August 9 in the professional journal Neuron, is the first of its kind to analyze signals associated with metacognition — a person’s ability to monitor and control cognition (a term cleverly described by researchers as “thinking about thinking.”)

“The brain has to keep track of decisions and the outcomes they produce,” said Marc Sommer, who did his research for the study as a University of Pittsburgh neuroscience faculty member and is now on the faculty at Duke University. “You need that continuity of thought,” Sommer continued. “We are constantly keeping decisions in mind as we move through life, thinking about other things. We guessed it was analogous to working memory, which would point toward the prefrontal cortex.”

Sommer predicted that neuronal correlates of metacognition resided in the same brain areas responsible for cognition, including the frontal cortex — a part of the brain linked with personality expression, decision making, and social behavior. Sommer worked with Paul G. Middlebrooks, who did his research for the study at Pitt before he received his Pitt PhD in neuroscience in 2011; Middlebrooks is now a postdoctoral fellow at Vanderbilt University. The research team studied single neurons in vivo in three frontal cortical regions of the brain: the frontal eye field (associated with visual attention and eye movements), the dorsolateral prefrontal cortex (responsible for motor planning, organization, and regulation), and the supplementary eye field (SEF) involved in the planning and control of saccadic eye movements, which are the extremely fast movements of the eye that allow it to continually refocus on an object.

To learn where metacognition occurs in the brain, subjects performed a visual decision-making task that involved random flashing lights and a dominant light on a cardboard square. Participants were asked to remember and pinpoint where the dominant light appeared, guessing whether they were correct. The researchers found that while neural activity correlated with decisions and guesses in all three brain areas, the putative metacognitive activity that linked decisions to bets resided exclusively in the SEF.

“The SEF is a complex area [of the brain] linked with motivational aspects of behavior,” said Sommer. “If we think we’re going to receive something good, neuronal activity tends to be high in SEF. People want good things in life, and to keep getting those good things, they have to compare what’s going on now versus the decisions made in the past.”

Sommer noted that defining such concepts related to metacognition, like consciousness, has been difficult for decades. He sees his research and future work related to studying metacognition as one step in a systematic process of working toward a better understanding of consciousness. By studying metacognition, he says, he reduces the big problem of studying a “train of thought” into a simpler component: examining how one cognitive process influences another.

“Why aren’t our thoughts independent of each other? Why don’t we just live in the moment? For a healthy person, it’s impossible to live in the moment. It’s a nice thing to say in terms of seizing the day and enjoying life, but our inner lives and experiences are much richer than that.”

So far, patients with mental disorders have not been tested on these tasks, but Sommer is interested to see how SEF and other brain areas might be disrupted in these disorders.

“With schizophrenia and Alzheimer’s disease, there is a fracturing of the thought process. It is constantly disrupted, and despite trying to keep a thought going, one is distracted very easily,” Sommers said. “Patients with these disorders have trouble sustaining a memory of past decisions to guide later behavior, suggesting a problem with metacognition.”

Funding for this research was provided by the University of Pittsburgh, the joint University of Pittsburgh-Carnegie Mellon University Center for the Neural Basis of Cognition, the National Institute of Mental Health, and the Alfred P. Sloan Foundation.

ScienceDaily (Aug. 9, 2012) — During the breeding season, polygynous male pectoral sandpipers that sleep the least sire the most young. A team of researchers headed by Bart Kempenaers from the Max Planck Institute for Ornithology in Seewiesen has now discovered this extraordinary relationship. During three weeks of intense competition under the constant daylight of the Arctic summer, males actively court females and compete with other males.

Courtship flight: This male is trying to impress any watching female sandpipers with its feats of flight and inflated chest. (Credit: Wolfgang Forstmeier)

Using an innovative combination of tags that monitored movement, male-female interactions, and brain activity in conjunction with DNA paternity testing, the authors discovered that the most sleepless males were the most successful in producing young. As the first evidence for adaptive sleep loss, these results challenge the commonly held view that reduced performance is an evolutionarily inescapable outcome of sleep loss.

Sometimes it would be nice to have 24 hours available to finish the workload of the day. However, the drive for sleep inevitably compromises our performance or even causes us to fall asleep under dangerous situations, such as driving a car. Daily sleep is therefore thought to be essential for regenerating the brain and maintaining performance. This holds true both for humans and other animals. Researchers led by Bart Kempenaers from the Max Planck Institute for Ornithology in Seewiesen have now found that during the three-week mating period male pectoral sandpipers (Calidris melanotos) are active for up to 95% of the time. This is even more remarkable considering the fact that the birds have just arrived in their breeding area in Alaska, after migrating from their overwintering grounds in the southern hemisphere.

Pectoral sandpipers have a polygynous mating system where one male mates with several females. Because males do not engage in parental care, a male’s reproductive success is determined exclusively by his access to fertile females. However, gaining this access is not that easy for pectoral sandpipers: “Males have to constantly repel their rivals through male-male competition and simultaneously convince females with intensive courtship display,” says director Bart Kempenaers. Given that the sun never sets during the Arctic summer, males that can engage in this extreme competition 24/7 should be at an advantage.

Indeed, the researchers found that the most active males interacted most with females and sired the most offspring. Paternity was determined by collecting DNA from all males, all females, and all offspring in the study area. To measure activity patterns, the researchers attached transmitters to the feathers of all males and most of the females. These radiotelemetry based senders allowed the team to monitor whether the animal was moving or resting. Finally, recordings of brain and muscle activity confirmed that active birds were awake and that inactive birds were in fact sleeping.

The brain activity recordings also reveal variation in sleep intensity: “Males that slept the least had the deepest sleep,” says co-author Niels Rattenborg who conducts sleep research at Seewiesen. Although this suggests that the birds might compensate for sleep loss by sleeping deeper, the researchers found that even when this was taken into consideration, the birds were still experiencing a deficit in sleep.

Based on the team’s data on birds that returned to the study area across breeding seasons, this reproductive sleep loss apparently has no long-term adverse impact on survival. On the contrary, successful males returned to the breeding area more often when compared to males siring less offspring and were more likely to sire offspring in their second year. Does the study question the dominant view that the function of sleep is to regenerate the brain? The researchers do not wish to go that far, although the findings clearly show that under certain circumstances animals may be able to evolve the ability to forgo, or postpone, large amounts of sleep while maintaining high neurobehavioral performance.

Importantly, the finding that not every male does this, even when there are fertile females around, suggests that “Long sleeping males may lack genetic traits that enable short sleeping individuals to maintain high performance despite a lack of sleep,” argues Bart Kempenaers. The researchers believe that determining why only some males engage in this adaptive sleeplessness may provide insight into the evolution of this extreme behaviour, as well as the ongoing debate over the functions of sleep and its relationship to health and longevity in humans.

ScienceDaily (Aug. 7, 2012) — Scientists from The Scripps Research Institute have identified a new stem cell population that may be responsible for giving birth to the neurons responsible for higher thinking. The finding also paves the way for scientists to produce these neurons in culture — a first step in developing better treatments for cognitive disorders, such as schizophrenia and autism, which result from disrupted connections among these brain cells.

Published in the August 10, 2012 issue of the journal Science, the new research reveals how neurons in the uppermost layers of the cerebral cortex form during embryonic brain development.

“The cerebral cortex is the seat of higher brain function, where information gets integrated and where we form memories and consciousness,” said the study’s senior author Ulrich Mueller, a professor and director of the Dorris Neuroscience Center at Scripps Research. “If we want to understand who we are, we need to understand this area where everything comes together and forms our impression of the world.”

In the new study, Mueller’s team identified a neural stem cell in mice that specifically gives rise to the neurons that make up the upper layers of the cerebral cortex. Previously, it was thought that all cortical neurons — those making up both the lower and upper layers — came from the same type of stem cell, called a radial glial cell, or RGC. A neuron’s fate was thought to be determined by the timing of its birth date. The Scripps Research team, however, showed that there is a distinct stem cell progenitor that gives rise to upper layer neurons, regardless of birth date or place.

“Advanced functions like consciousness, thought, and creativity require a lot of different neuronal cell types and a central question has been how all this diversity is produced in the cortex,” said Santos Franco, a senior research associate in Mueller’s laboratory and first author of the paper. “Our study shows this diversity already exists in the progenitor cells.”

Peeling Back the Onion Layers

In mammals, the cortex is made up of six distinct anatomic layers holding different types of excitatory neurons. They are not the uniform layers of a cake, but rather, they are more like the layers wrapped around an onion. The smaller lower layers, on the inside, host neurons that connect to the brain stem and spinal cord to help regulate essential functions such as breathing and movement. The larger upper layers, closer to the outer surface of the brain, contain neurons that integrate information coming in from the senses and connect across the two halves of the brain.

The upper layers are a “relatively young invention,” evolutionarily speaking, having been greatly expanded during primate evolution, said Mueller. They give humans in particular the unique abilities to think abstractly, plan for the future and problem-solve.

For the last two decades, scientists have believed that the fate of cerebral cortex neurons was determined by their birth date because each layer is formed in a time-dependent manner. The lower layer neurons form in the center of the “ball” first, and then the cells that will become the upper layers form last, migrating through the lower layers.

“So the model was that there is a stem cell in the center of the ball that generates the different types of neurons in successive waves,” said Mueller. “What we now show is that there are at least two different populations of RGCs and potentially more.”

Following Fate

Franco first created a line of mice in which he could track upper-layer neurons as they were born and migrated. The team followed a marker gene called Cux2, which was previously reported to be expressed only by upper-layer neurons. By linking a gene for an enzyme called Cre to the Cux2 gene, the scientists could watch any cell expressing Cux2 under the microscope, because the Cre enzyme flips on another gene that glows fluorescent red.

Surprisingly, the team observed Cux2 already turned on in some of the RGCs, even at the earliest points in brain development — embryonic day nine or ten — before any upper-layer neurons exist. Following this population of glowing stem cells through development, the team showed that the cells almost exclusively generated upper-layer neurons. In contrast, the subgroup of RGCs not expressing Cux2 became lower-layer neurons.

Next, the team removed these Cux2-positive precursor cells from their niche in the embryonic brain to see how they would develop in a lab dish. When they cultured both types of RGCs, again only Cux2-expressing RGCs developed into upper-layer neurons.

In developing brains, these Cux2-positive stem cells first self-renew and proliferate before differentiating later into neurons. So, the team wanted to know if a neuron’s birth date determined its fate. To test this, the researchers delivered a TCF4 molecule in utero that forced the Cux2-positive RGCs to prematurely differentiate. Even though it was too early in normal development, the Cux2-positive RGCs still produced upper-layer neurons.

In other words, regardless of position or timing, the Cux2-positive RGCs are destined to become upper-layer neurons. Mueller and colleagues concluded that these stem cells have some intrinsic property that determines their fate from the start.

The work also shows that this RGC subset is responsible for the huge proliferation of cells necessary to create the larger upper-layer cortex found in primate brains. “If we want to understand how the human brain evolved, how we are different from an amphibian, then this one precursor cell may have been important,” said Mueller.

But, bigger brains came with a risk, making humans more prone to disorders when upper-layer neurons don’t form connections properly. Up until now, researchers trying to reproduce human cortical neurons in the lab from stem cells have only generated lower-layer-type neurons. “This opens a door now to try to make the upper-layer neurons, which are frequently affected in psychiatric disorders,” said Mueller.

In addition to Mueller and Franco, authors of the paper, “Fate-restricted neural progenitors in the mammalian cerebral cortex,” were Cristina Gil-Sanz, Isabel Martinez-Garay, Ana Espinosa, Sarah R. Harkins-Perry, and Cynthia Ramos of Scripps Research. Martinez-Garay is now at the University of Oxford.

This research was supported by the Dorris Neuroscience Center, US National Institutes of Health (grant award numbers NS060355, NS046456, MH078833), and California Institute for Regenerative Medicine, and conducted in affiliation with the NIH Blueprint-funded Cre Driver Network.

ScienceDaily (Aug. 8, 2012) — The family of small insectivores, Talpidae, includes the moles, shrew moles, and aquatic desmans. New research published in BioMed Central’s open access journalEvoDevo has found that the enlargement of moles’ digging front paws, compared to their feet, is controlled by altered timing of expression of the gene SOX9.

Talpaeuropaea. (Credit: Image courtesy of BioMed Central)

Fossorial (digging) moles are closely related to shrews, however adaption to burrowing underground has given them specialized strong forelegs, and large, broad hands with a rotated palm. Moles also have an extra digit-like structure in both hands and feet (Os falciforme), which presumably helps with digging.

SOX genes are transcription factors and consequently, when they bind to DNA, they regulate the expression of other genes. SOX9 is specifically involved in chondrocyte (cartilage) differentiation and is also involved in the development of the Os falciforme.

When a multinational team of researchers compared the timing and pattern of SOX9 expression during development of the hands and feet of the Iberian mole (Talpa occidentalis), shrew (Cryptotis parva), and mouse (Mus musculus) they realized that there was a difference in timing of SOX9 expression between the species. SOX9 is expressed at the same time during embryo development in front and hind paws for both mice and shrews but occurs sooner in the hands of moles than their developing feet.

Dr Constanze Bickelmann, from the Paleontological Institute and Museum, University of Zurich, explained, “This difference in timing of expression of a gene is called transcriptional heterochrony. It is an extreme example of adaption to an ecological niche, in this case digging, which has selected for animals with bigger front paws, who were better diggers and so on.”

Since moles evolutionary split from shrews about 70 million years ago, this selection process has led to a slow, but profound, change to the expression of a protein found in nearly all animal species.

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The above story is reprinted from materials provided byBioMed Central.

ScienceDaily (Aug. 8, 2012) — Vaginal birth triggers the expression of a protein in the brains of newborns that improves brain development and function in adulthood, according to a new study by Yale School of Medicine researchers, who also found that this protein expression is impaired in the brains of offspring delivered by caesarean section (C-sections).

These findings are published in the August issue of PLoS ONE by a team of researchers led by Tamas Horvath, the Jean and David W. Wallace Professor of Biomedical Research and chair of the Department of Comparative Medicine at Yale School of Medicine.

The team studied the effect of natural and surgical deliveries on mitochondrial uncoupling protein 2 (UCP2) in mice. UCP2 is important for the proper development of hippocampal neurons and circuits. This area of the brain is responsible for short- and long-term memory. UCP2 is involved in cellular metabolism of fat, which is a key component of breast milk, suggesting that induction of UCP2 by natural birth may aid the transition to breast feeding.

The researchers found that natural birth triggered UCP2 expression in the neurons located in the hippocampal region of the brain. This was diminished in the brains of mice born via C-section. Knocking out the UCP2 gene or chemically inhibiting UCP2 function interfered with the differentiation of hippocampal neurons and circuits, and impaired adult behaviors related to hippocampal functions.

“These results reveal a potentially critical role of UCP2 in the proper development of brain circuits and related behaviors,” said Horvath. “The increasing prevalence of C-sections driven by convenience rather than medical necessity may have a previously unsuspected lasting effect on brain development and function in humans as well.”

Other authors on the study included Julia Simon-Areces, Marcelo O. Dietrich, Gretchen Hermes, Luis Miguel Garcia-Segura, and Maria-Angeles Arevalo.The study was funded by the National Institutes of Health.

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The above story is reprinted from materials provided byYale University. The original article was written by Karen N. Peart.

ScienceDaily (Aug. 9, 2012) — A scientist from the Senckenberg Research Institute in Frankfurt has discovered the first eyeless huntsman spider in the world. The accompanying study has been published by the scientific journal Zootaxa.

With a leg span of only six centimetres and a body size of around twelve millimetres, the spiderSinopoda scurion is certainly not one of the largest representatives of the huntsman spiders, which include more than 1100 species. However, it is the first of its kind in the world without any eyes.

“I found the spider in a cave in Laos, around 100 kilometres away from the famous Xe Bang Fai cave,” reports Peter Jäger, head of the arachnology section at the Senckenberg Research Institute in Frankfurt. “We already knew of spiders of this genus from other caves, but they always had eyes and complete pigmentation. Sinopoda scurion is the first huntsman spider without eyes.”

The regression of the eyes is attributable to living permanently without daylight. This adaptation was also observed in other cave-dwelling spider species by the Frankfurt arachnologist. “The Sinopodaspecies described demonstrate all kinds of transitions to cave adaptation — from eight functioning eyes to forms with six, four and two lenses, right up to blind spiders,” explains Jäger.

The spiders are in good company: fish, scorpions and crabs that have adapted to caves have already been found in the caves of Laos.

In total, the Frankfurt spider researchers have described nine new species of the genus Sinopoda. The fact that all of the species have been found in caves confirms the animals’ preference for underground habitats. Because of the small-scale area in which the spider species can be found it is possible to study their adjustment to the cave as a dwelling — the number of eyes present and the visual faculty may possibly shed light on the time of settlement. “Furthermore, the spiders can be used as indicators for the threat to their habitats. These are often endangered by tourism or the exploitation of the limestone rocks to make cement,” says Jäger.

The eyeless huntsman spider was named after the Swiss company “Scurion” that makes headlamps for caves. “Sinopoda scurion is the first species that I have named after a company in the context of the Patrons for Biodiversity programme,” explains Jäger. “The headlamps by Scurion help me to illuminate the darkest corners on my cave trips, and thus recognise hazards such as poisonous snakes and scorpions, but also discover very small organisms.”

ScienceDaily (Aug. 8, 2012) — What mechanisms control the generation and maintenance of biological diversity on the planet?

A small clam attached to its mud shrimp host. This species of clam, Neaeromya rugifera, is part of the Galeommatoidea superfamily. (Credit: Photo by Jingchun Li)

It’s a central question in evolutionary biology. For land-dwelling organisms such as insects and the flowers they pollinate, it’s clear that interactions between species are one of the main drivers of the evolutionary change that leads to biological diversity.

But the picture is much murkier for ocean dwellers, mainly because the scope of ecological interactions remains poorly characterized for most marine species. In one of the first efforts to examine how species interactions drive diversification of ocean-dwelling organisms, two University of Michigan researchers and an Australian colleague looked at the lifestyle choices within an exceptionally diverse superfamily of tiny clams, the Galeommatoidea.

They found that the fingernail-size-and-smaller clams’ propensity to shack up with much larger, burrowing creatures such as sea urchins, shrimp and worms was a key adaptation that led to the evolutionary success of the superfamily, as measured by its “megadiverse” status among marine bivalves. There are about 500 described species of galeommatoidean clams and many more undescribed species.

By becoming the uninvited house guests of their burrowing hosts, these freeloading, thin-shelled clams acquire a safe haven from predators prowling soft-bottomed sediments, where there’s nowhere else to hide. Gaining this deep refuge opened up a vast habitat type — soft-bottom marine sediments composed of sand, silt and clay — that would otherwise have remained unavailable to these clams.

Galeommatoidean clams are found worldwide in all the major ocean basins, in both rocky and soft-bottom habitats. Some of the clams live a solitary existence, while others form so-called commensal relationships with larger invertebrate hosts. A commensal relationship is one in which one organism benefits and the other is not harmed.

In a study scheduled for online publication Aug. 8 in the journal PLoS ONE, the U-M-led team performed a statistical analysis of the lifestyle and habitat preferences of 121 galeommatoidean species based on 90 source documents.

The researchers found that all but two of the 57 free-living species were restricted to hard-bottom habitats, typically hidden in rocky or coral-reef crevices. In contrast, 56 of the 60 commensal species were soft-sediment dwellers.

The results show that formation of commensal associations by galeommatoidean clams is robustly correlated with living in sediments. That finding is consistent with the hypothesis that evolution of these commensal relationships was primarily an adaptation to living in soft-bottom habitats.

“What was surprising was the overwhelming evidence that commensalism is associated with the soft-bottomed habitat. You seldom get such clear-cut data in an ecological study,” said Jingchun Li, a doctoral student in the U-M Department of Ecology and Evolutionary Biology and first author of the PLoS ONE paper.

Clams and other bivalves have evolved two general anti-predator strategies: armor (think oysters) and avoidance. Since galeommatoidean clams have fragile shells, they must go the avoidance route, and following a larger host into a burrow allows the clams to attain depths of up to 3 feet — hundreds of times their body lengths.

Galeommatoidean clams lack the siphons (often called necks) that other clams use to feed and breathe while remaining safely buried in the sand. Siphons consist of two tubes: Water enters the clam’s body through one siphon, flowing into gills that capture oxygen and trap food. The water then flows out of the clam through the other siphon.

The siphon-less galeommatoideans make up for that shortcoming by teaming up with hosts that constantly pump fresh seawater into, through, and then out of their burrows.

“This allows the clams to stay deep and safe, while still having access to water and oxygen and a food supply,” Li said. In this way, the hosts act as giant siphon substitutes for the tiny clams.

“Jingchun’s finding that the type of sea floor habitat strongly modulates the ecological importance of commensalism in these megadiverse clams gives us a novel insight into how ostensibly irrelevant background physical conditions may shape the evolution of species interactions in marine environments,” said study co-author Diarmaid O’Foighil, Li’s adviser and the director of the U-M Museum of Zoology.

The second phase of the clam study will test the relative importance of free-living and commensal lifestyles in driving galeommatoidean diversification. Using data from about 300 species, the researchers will construct a phylogenetic tree for the entire superfamily.

The third author of the PLoS ONE paper is Peter Middelfart of the Australian Museum.

The study is supported by a Rackham International Student Fellowship from the University of Michigan, a Molluscan Research Grant from the Malacological Society of Australasia, and a grant from the National Science Foundation.